tbuckley/cabot-search huggingface dataset:
Viral protease cleavage of MAVS in genetically modified mice with hepatitis A virus infection
Authors: Lu Sun, Hui Feng, Ichiro Misumi, Takayoshi Shirasaki, Lucinda Hensley, Olga González-López, Itoe Shiota, Wei-Chun Chou, Jenny P.-Y. Ting, John M. Cullen, Dale O. Cowley, Jason K. Whitmire, Stanley M. Lemon
Journal: Journal of Hepatology (2022)
Long-acting PFI-2 small molecule release and multilayer scaffold design achieve extensive new formation of complex periodontal tissues with unprecedented fidelity
Authors: Huling Lyu, Xuefeng Zhou, Yunzhu Qian, Xiaohua Liu, Gokul Gopinathan, Mirali Pandya, Chunlin Qin, Xianghong Luan, Thomas G.H. Diekwisch
Journal: Biomaterials (2022)

The faithful engineering of complex human tissues such as the bone/soft tissue/mineralized tissue interface in periodontal tissues requires innovative molecular cues in conjunction with tailored scaffolds. To address the loss of periodontal bone and connective tissues following periodontal disease, we have generated a polydopamine and collagen coated electrospun PLGA-PCL (PP) scaffold enriched with the small molecule mediator PFI-2 (PP-PFI-pDA-COL-PFI). In vitro 3D studies using PDL progenitors revealed that the PP-PFI-pDA-COL-PFI scaffold substantially enhanced Alizarin Red staining, increased Ca/P ratios 4-fold, and stimulated cell proliferation more than 12-fold compared to PP-controls, suggestive of its potential for mineralized tissue engineering. When applied in our experimental periodontitis model, the PP-PFI-pDA-COL-PFI scaffold resulted in a substantial 34% reduction in alveolar bone defect height, a 25% root-length gain in periodontal attachment, and the formation of highly ordered regenerated acellular cementum twice as thick as in controls. Explaining the mechanism of PFI-2 mineralized tissue regeneration in periodontal tissues, PFI-2 inhibited SETD7-mediated β-Catenin protein methylation and increased β-Catenin nuclear localization. Together, dual-level PFI-2 incorporation into a degradable, dopamine/collagen coated PLGA/PCL scaffold backbone resulted in the regeneration of the tripartite periodontal complex with unprecedented fidelity, including periodontal attachment and new formation of mineralized tissues in inflamed periodontal environments.
Reverse inflammaging: Long-term effects of HCV cure on biological age
Authors: Carlos Oltmanns, Zhaoli Liu, Jasmin Mischke, Jan Tauwaldt, Yonatan Ayalew Mekonnen, Melanie Urbanek-Quaing, Jennifer Debarry, Benjamin Maasoumy, Heiner Wedemeyer, Anke R M Kraft, Cheng-Jian Xu, Markus Cornberg
Journal: Journal of Hepatology (2022)
Severity of systemic inflammation is the main predictor of ACLF and bleeding in individuals with acutely decompensated cirrhosis
Authors: Alberto Zanetto, Filippo Pelizzaro, Elena Campello, Cristiana Bulato, Lorenz Balcar, Wenyi Gu, Sabrina Gavasso, Graziella Saggiorato, Stefan Zeuzem, Francesco Paolo Russo, Mattias Mandorfer, Thomas Reiberger, Jonel Trebicka, Patrizia Burra, Paolo Simioni, Marco Senzolo
Journal: Journal of Hepatology (2022)
Urinary Zinc and Incident Type 2 Diabetes: Prospective Evidence From the Strong Heart Study
Authors: Marta Galvez-Fernandez, Martha Powers, Maria Grau-Perez, Arce Domingo-Relloso, Nancy Lolacono, Walter Goessler, Ying Zhang, Amanda Fretts, Jason G. Umans, Nisa Maruthur, Ana Navas-Acien
Journal: Diabetes Care (2022)

OBJECTIVE Hyperglycemia can increase urinary zinc excretion. We evaluated the association of higher urinary zinc level with new diagnosis of incident type 2 diabetes mellitus (T2DM) in adult populations with a high burden of T2DM from AZ, OK, and ND and SD. We also assessed the cross-sectional association of urinary zinc levels with prevalent prediabetes. RESEARCH DESIGN AND METHODS We included 1,339 adults free of T2DM at baseline (1989–1991) followed through 1998–1999 in the Strong Heart Study (SHS) and 1,905 family members of SHS participants followed as part of the Strong Heart Family Study (SHFS) through 2006–2009. RESULTS T2DM incidence was 14.7% (mean follow-up 6.6 years) in the SHS and 13.5% (mean follow-up 5.6 years) in the SHFS. After adjustment for sex, site, education, smoking status, BMI, and estimated glomerular filtration rate, the hazard ratio of T2DM in comparing 75th vs. 25th percentiles of urinary zinc distribution was 1.21 (95% CI 1.08, 1.36) in the SHS and 1.12 (0.96, 1.31) in the SHFS. These associations were attenuated but significant in the SHS after adjustment for HOMA of insulin resistance (HOMA-IR) score. With exclusion of participants with prediabetes at baseline, urinary zinc remained significantly associated with T2DM in the SHS. In cross-sectional analyses, prediabetes was associated with higher urinary zinc levels. CONCLUSIONS Urinary zinc levels were associated with T2DM incidence and prediabetes prevalence even after adjustment for HOMA-IR in populations with a high burden of T2DM. These results highlight the importance of zinc metabolism in diabetes development.
Re: James W.F. Catto, Pramit Khetrapal, Federico Ricciardi, et al. Effect of Robot-assisted Radical Cystectomy with Intracorporeal Urinary Diversion vs Open Radical Cystectomy on 90-Day Morbidity and Mortality Among Patients with Bladder Cancer: A Randomized Clinical Trial. JAMA 2022;327:2092–103
Authors: Bernardo Rocco, Maria Chiara Sighinolfi
Journal: European Urology (2022)
Genomic characteristics of a notable emerging serotype O10:K4 of Vibrio parahaemolyticus from food-borne cluster events in Guangzhou, China
Authors: Peng He, Jing Zhang, Yong Zhou, Shuiping Hou, Xia Tao, Anna Wang, Zhicong Yang, Zhijun Bai, Xinwei Wu
Journal: Journal of Infection (2022)
The value of broad taxonomic comparisons in evolutionary medicine: Disease is not a trait but a <i>state of a trait</i>!
Authors: Mihaela Pavličev, Günter P. Wagner
Journal: MedComm (2022)

Abstract In this short paper, we argue that there is a fundamental connection between the medical sciences and evolutionary biology as both are sciences of biological variation. Medicine studies pathological variation among humans (and domestic animals in veterinary medicine) and evolutionary biology studies variation within and among species in general. A key principle of evolutionary biology is that genetic differences among species have arisen first from mutations originating within populations. This implies a mechanistic continuity between variation among individuals within a species and variation between species. This fact motivates research that seeks to leverage comparisons among species to unravel the genetic basis of human disease vulnerabilities. This view also implies that genetically caused diseases can be understood as extreme states of an underlying trait, that is, an axis of variation, rather than distinct traits, as often assumed in GWAS studies. We illustrate these points with a number of examples as diverse as anatomical birth defects, cranio‐facial variation, preeclampsia and vulnerability to metastatic cancer.
Clusters of Rapid HIV Transmission Among Gay, Bisexual, and Other Men Who Have Sex with Men — United States, 2018–2021
Authors: Stephen M. Perez, Nivedha Panneer, Anne Marie France, Neal Carnes, Kathryn G. Curran, Damian J. Denson, Alexandra M. Oster
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Gay, bisexual, and other men who have sex with men (MSM) accounted for 68% of new HIV diagnoses in the United States in 2020* (1). Despite advances in treatment and prevention, HIV transmission among MSM continues, in part because of stigma and barriers to accessing prevention and treatment services (2). HIV cluster detection and response, a core strategy of the Ending the HIV Epidemic in the United States initiative,† is an important tool for early identification and response to rapid HIV transmission, including among MSM. To better understand rapid HIV transmission among this population, CDC characterized large HIV molecular clusters detected using analysis of HIV-1 nucleotide sequence data from the National HIV Surveillance System (NHSS).§ Among 38 such clusters first detected during 2018-2019 that had grown to include more than 25 persons by December 2021, 29 occurred primarily among MSM. Clusters primarily among MSM occurred in all geographic regions, and 97% involved multiple states. Clusters were heterogeneous in age, gender identity, and race and ethnicity and had rapid growth rates (median = nine persons added per year). The overall transmission rate at cluster detection was 22 transmission events per 100 person-years, more than six times that of previously estimated national transmission rates (3). Most clusters of rapid HIV transmission occur among MSM. Swift response to reach diverse persons and communities with early, tailored, and focused interventions is essential to reducing HIV transmission (4).
<i>Notes from the Field: </i>Norovirus Outbreaks Reported Through NoroSTAT — 12 States, August 2012–July 2022
Authors: Anita K. Kambhampati, Mary E. Wikswo, Leslie Barclay, Jan Vinjé, Sara A. Mirza, Esther Rei, Brandon Sabina, Jennifer Beggs, Diana K. Riner, Elizabeth Cebelinski, Amy Saupe, Amanda Bartling, Brianna K.D. Loeck, Nicole Chase, Jessica Houston, Eric Brandt, Ellen Salehi, Emilio DeBess, Laura Tsaknaridis, Gregory Goodwin, Hani Mohamed, Mugdha Golwalkar, Linda Thomas, Mary Kathryne Donnelly, Haley Greene, Timothy Davis, Lynn Roberts, Rob Christensen, Matthew Peterson
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Norovirus is the leading cause of acute gastroenteritis in the United States (1).In April 2020, the incidence of norovirus outbreaks in the United States declined substantially, likely because of implementation of COVID-19-related nonpharmaceutical interventions, such as facility closures, social distancing, and increased hand hygiene (2).Similar declines were observed in other countries (3,4).Norovirus outbreaks in the United States increased rapidly starting in January 2022, approaching prepandemic (i.e., 2012-2019) levels.Norovirus transmission can be prevented by thorough handwashing and proper cleaning and disinfection of contaminated surfaces.In 2012, CDC established the Norovirus Sentinel Testing and Tracking Network (NoroSTAT) to improve timeliness and completeness of surveillance for norovirus outbreaks that occur in the United States.NoroSTAT is a collaboration between CDC and 12 state health departments.*Outbreaks are defined as two or more cases of illness associated with a common exposure.NoroSTAT-participating states report a minimum set of data elements † to the National Outbreak Reporting System § for all confirmed norovirus outbreaks (i.e., outbreaks with two or more laboratory-confirmed norovirus cases) and suspected norovirus outbreaks (i.e., outbreaks with fewer than two laboratory-confirmed norovirus cases) within 7 business days of notification.These states also upload typing information for norovirus-positive outbreak specimens to CaliciNet, ¶ the national norovirus laboratory surveillance network, within 7 business days of receipt of two * Massachusetts, Michigan, Minnesota, Nebraska, New Mexico, Ohio, Oregon, South Carolina, Tennessee, Virginia, Wisconsin, and Wyoming.† Within 7 business days of health department notification, NoroSTATparticipating states are required to report the following data elements to CDC for all norovirus outbreaks: state report ID, primary mode of outbreak transmission, date of first illness onset (at the time of initial report), date of notification to state health department, state in which the outbreak exposure occurred, estimated total number of primary ill cases, confirmed or suspected etiology, and outbreak setting.
Anti-BCMA CAR-T cells therapy for a patient with extremely high membrane BCMA expression: a case report
Authors: Dan Li, Yimei Que, Shengnan Ding, Guang Hu, Wen Wang, Xia Mao, Ying Wang, Chunrui Li, Liang Huang, Jianfeng Zhou, Wei Zhang, Min Xiao
Journal: Journal for ImmunoTherapy of Cancer (2022)

B cell maturation antigen (BCMA)-directed CAR-T cell therapy is a disruptive approach for treating relapsed/refractory multiple myeloma (R/R MM); however, optimization is necessary to maximize patient benefit. We report the case of a 61-year-old woman with primary refractory MM who presented with high expression of membrane BCMA and low expression of soluble BCMA (sBCMA), experienced grade 4 cytokine release syndrome, and died fromsevere pneumonia after receiving anti-BCMA CAR-T (CT103A) therapy. This case highlights the importance of assessing the expression range of BCMA for its efficacy and safety in patients receiving BCMA CAR-T therapy. For patients who present with extremely high membrane BCMA expression and extremely low sBCMA expression, the presence of γ-secretase-related gene mutations should be considered. Special attention should also be paid to the prevention and treatment of cytokine release syndrome in such patients.
Shorter versus longer corticosteroid duration and recurrent immune checkpoint inhibitor-associated AKI
Authors: Shruti Gupta, Clara Garcia-Carro, Jason M Prosek, Ilya Glezerman, Sandra M Herrmann, Pablo Garcia, Ala Abudayyeh, Nuttha Lumlertgul, A Bilal Malik, Sebastian Loew, Pazit Beckerman, Amanda D Renaghan, Christopher A Carlos, Arash Rashidi, Zain Mithani, Priya Deshpande, Sunil Rangarajan, Chintan V Shah, Sophie De Seigneux, Luca Campedel, Abhijat Kitchlu, Daniel Sanghoon Shin, Gaia Coppock, David I Ortiz-Melo, Ben Sprangers, Vikram Aggarwal, Karolina Benesova, Rimda Wanchoo, Naoka Murakami, Frank B Cortazar, Kerry L Reynolds, Meghan E Sise, Maria Jose Soler, David E Leaf
Journal: Journal for ImmunoTherapy of Cancer (2022)

Background Corticosteroids are the mainstay of treatment for immune checkpoint inhibitor-associated acute kidney injury (ICPi-AKI), but the optimal duration of therapy has not been established. Prolonged use of corticosteroids can cause numerous adverse effects and may decrease progression-free survival among patients treated with ICPis. We sought to determine whether a shorter duration of corticosteroids was equally efficacious and safe as compared with a longer duration. Methods We used data from an international multicenter cohort study of patients diagnosed with ICPi-AKI from 29 centers across nine countries. We examined whether a shorter duration of corticosteroids (28 days or less) was associated with a higher rate of recurrent ICPi-AKI or death within 30 days following completion of corticosteroid treatment as compared with a longer duration (29–84 days). Results Of 165 patients treated with corticosteroids, 56 (34%) received a shorter duration of treatment and 109 (66%) received a longer duration. Patients in the shorter versus longer duration groups were similar with respect to baseline and ICPi-AKI characteristics. Five of 56 patients (8.9%) in the shorter duration group and 12 of 109 (11%) in the longer duration group developed recurrent ICPi-AKI or died (p=0.90). Nadir serum creatinine in the first 14, 28, and 90 days following completion of corticosteroid treatment was similar between groups (p=0.40, p=0.56, and p=0.89, respectively). Conclusion A shorter duration of corticosteroids (28 days or less) may be safe for patients with ICPi-AKI. However, the findings may be susceptible to unmeasured confounding and further research from randomized clinical trials is needed.
Ablation of the endoplasmic reticulum stress kinase PERK induces paraptosis and type I interferon to promote anti-tumor T cell responses
Authors: Jessica K Mandula, Shiun Chang, Eslam Mohamed, Rachel Jimenez, Rosa A Sierra-Mondragon, Darwin C Chang, Alyssa N Obermayer, Carlos M Moran-Segura, Satyajit Das, Julio A Vazquez-Martinez, Karol Prieto, Ann Chen, Keiran S M Smalley, Brian Czerniecki, Peter Forsyth, Richard C Koya, Brian Ruffell, Juan R Cubillos-Ruiz, David H Munn, Timothy I Shaw, Jose R Conejo-Garcia, Paulo C Rodriguez
Journal: Cancer Cell (2022)
MPS1 inhibition primes immunogenicity of KRAS-LKB1 mutant lung cancer
Authors: Shunsuke Kitajima, Tetsuo Tani, Benjamin F Springer, Marco Campisi, Tatsuya Osaki, Koji Haratani, Minyue Chen, Erik H Knelson, Navin R Mahadevan, Jessica Ritter, Ryohei Yoshida, Jens Köhler, Atsuko Ogino, Ryu-Suke Nozawa, Shriram K Sundararaman, Tran C Thai, Mizuki Homme, Brandon Piel, Sophie Kivlehan, Bonje N Obua, Connor Purcell, Mamiko Yajima, Thanh U Barbie, Patrick H Lizotte, Pasi A Jänne, Cloud P Paweletz, Prafulla C Gokhale, David A Barbie
Journal: Cancer Cell (2022)
Indoor visible moulds and rhinitis in adults: The <scp>EGEA</scp> study
Authors: Laurent Orsi, Marine Savouré, Jean Bousquet, Bénédicte Jacquemin, Valérie Siroux, Maritta S. Jaakkola, Jouni J. K. Jaakkola, Bénédicte Leynaert, Rachel Nadif
Journal: Allergy (2022)
Diagnostic value of a medical algorithm for investigation of perioperative hypersensitivity reactions
Authors: Asger Sverrild, John Carruthers, Kavitha Garuna Murthee, Alice Moore, Robyn Elizabeth O'Hehir, Robert Puy, Mark Hew, Celia Zubrinich
Journal: Allergy (2022)

Evaluation of perioperative hypersensitivity (POH) is challenging, and accurate screening tools are needed to optimize the diagnostic process. We aimed to assess and validate the diagnostic value of a published algorithm (using tryptase and clinical presentation) to identify appropriate individuals for further testing for IgE-mediated POH.We analysed the clinical presentation (tryptase elevation, cardiovascular, respiratory, skin involvement) of patients proceeding to testing for possible IgE-mediated POH at a single tertiary referral centre, relative to subsequent skin testing and specific IgE results. Clinical presentations by drug class were also determined.In 293 consecutive patients, the use of a published algorithm based on one or more of; (i) defined increase in serum tryptase, (ii) involvement of at least two-organ systems, or (iii) presentation with new urticaria and/or angioedema; was highly sensitive [98.8% (CI95: 95.7-99.9%)] but less specific [34.6% (CI95: 25.7-44.4%)] in identifying patients testing positive on skin testing and/or specific IgE. Presentation with cardiovascular symptoms was also sensitive [89.8%(CI95: 84.2-94.0%)], while the combination of respiratory symptoms and increased tryptase was most specific [85.9%(CI95:76.6-92.5%)]. Respiratory involvement was more common in neuromuscular blocking agent allergy, while urticaria/angioedema was more common in antibiotic allergy.The published algorithm (of tryptase rise, two-organ involvement or new urticaria/angioedema) is highly sensitive, and appropriate as a screening tool to identify patients suitable for testing for IgE-mediated POH.
CrossMoDA 2021 challenge: Benchmark of cross-modality domain adaptation techniques for vestibular schwannoma and cochlea segmentation
Authors: Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeon Gyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren
Journal: Medical Image Analysis (2022)

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.
Nucleoside‐modified mRNA vaccines yield robust blocking antibody responses against major house dust mite allergens
Authors: Sirikarn Jitthamstaporn, Rueangsit Inthong, Dittaya Audomsun, Supapich Chanasit, Chanatip Thanasarnthungcharoen, Paulo J. C. Lin, Drew Weissman, Norbert Pardi, Alain Jacquet
Journal: Allergy (2022)
Long covid—an update for primary care
Authors: Trisha Greenhalgh, Manoj Sivan, Brendan Delaney, Rachael Evans, Ruairidh Milne
Journal: BMJ (2022)

Ziauddeen N, Gurdasani D, O’Hara ME, et al. Characteristics of long covid: findings from a social media survey.medRxiv2021 [Preprint] doi:10.1136/jech-2021-SSMabstracts.194.
Multidimensional endotyping using nasal proteomics predicts molecular phenotypes in the asthmatic airways
Authors: Ioana Agache, Mohamed H. Shamji, Nazanin Zounemat Kermani, Giulia Vecchi, Alberto Favaro, Janice A. Layhadi, Anja Heider, Didem Sanver Akbas, Paulina Filipaviciute, Lily Y.D. Wu, Catalina Cojanu, Alexandru Laculiceanu, Cezmi A. Akdis, Ian M. Adcock
Journal: Journal of Allergy and Clinical Immunology (2022)